jalview

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Merge branch 'bug/JAL-3885_sequence_fetched_not_displaying_PFAM_Seed' into develop

JAL-2909 increase commandlinetests timeout

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    /test/jalview/bin/CommandLineOperations.java
JAL-2909 fix up tests and ensure we don’t test bam as a writable format

JAL-2909 pass a dummy sequence object to receive features. Ideally we should test that features look like they are expected too here !

JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop Merge remote-tracking branch 'origin/features/JAL-2909_bamImport2_11' into features/JAL-2909_bamImport_2_11_2

Conflicts:

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/FileFormat.java

src/jalview/io/FileLoader.java

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    /src/jalview/io/AlignmentFileReaderI.java
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    /src/jalview/io/AppletFormatAdapter.java
JAL-3885 Made the database JComboBox have StringPair entries to allow a display value, set to the single item dbname if there's a single item

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    /src/jalview/gui/SequenceFetcher.java
JAL-3884 squish alarming but harmless errors when uniprot doesn’t have a record

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    /src/jalview/ws/dbsources/Uniprot.java
JAL-3878 Add isInteractive() method to Operation interface.

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    /src/jalview/ws2/operations/Operation.java
JAL-3881 split on any nonalphanumeric symbol (plus _) to generate putative sequence identifiers with which to query databases

JAL-3829 report when 3d-beacons doesn’t provide any models

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    /src/jalview/gui/StructureChooser.java
JAL-3878 Add getName() to Operation interface.

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    /src/jalview/ws2/operations/Operation.java
JAL-3783 Updated groovy-all-2.4. Currently newer stable releases cause a problem with shadowJar.

    • binary
    /j11lib/groovy-all-2.4.21-indy.jar
    • binary
    /j8lib/groovy-all-2.4.21-indy.jar
JAL-3878 Wire web services logic to UI elements.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3746 update the example corefile for jalviewjs

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-3878 Fire service changed event after discovery task is done.

JAL-3878 Fix incorrect value of isRunning in SlivkaWSDiscoverer

JAL-3878 Move operation type from WebService to Operation.

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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Code reformatting.

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    /src/jalview/ws2/WebServiceDiscoverer.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/WebServiceInfoUpdater.java
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    /src/jalview/ws2/WebServiceWorkerI.java
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Display results of completed alignment job

JAL-3878 Change SERVER_ERROR.isSubmitted to false.

Some server errors may occur before the job is submitted.

It's safer to associate the error with the job not being

submitted.

Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3821 data file for failing test

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    /test/jalview/io/J03321_rna.embl.txt
JAL-3829 right click to view popup menu to show link - maybe better to have a link button in the table instead ?

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-3829 abstract essential TDB metadata from the user configurable data array displayed in the JTable

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    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
JAL-3878 Move WSJob instantiation out of WebService classes.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3594 added BG and UoD logo and banner to splashscreens, and adjusted status text box

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3821_reinstate_patch' into develop